Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Comment on "Why is the DNA denaturation transition first order?"

In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical experiments. In the added last paragraph, we point out that for real DNA the average distance between denatured loops is not of the order of the persistence length of a single-stranded chain but much larger. This corroborates our reasoning that the double helix between loops is quite rigid, and thereby our conclusion.Comment: 1 page, REVTeX. Last paragraph adde

Concept and Practice in Community Mobilization for Health: A Qualitative Evaluation of the Brantford COMMIT Smoking Cessation Intervention Trial

The Community Intervention Trial for Smoking Cessation (COMMIT) was one of the largest health promotion interventions in North America. Using 11 pairs of matched intervention and control communities, the U.S. National Cancer Institute sought to establish the viability of a community-based approach to smoking cessation, with the expectation of significant impacts on cessation rates amongst heavy smokers during the four years of intervention. The evaluation components of the COMMIT trial relied primarily on the use of surveys to document quantitative changes in attitudes, beliefs and behaviours. A complementary ancillary qualitative evaluation was conducted by the author in the only Canadian intervention site in the trial in Brantford, Ontario. Depth interviews and focus groups were conducted with 45 members of a Smokers' Network established by COMMIT. Subsequently, 35 intervention staff, researchers and community influential were interviewed. Transcripts were coded and analyzed using qualitative analysis software. Several objectives guided the qualitative evaluation study in Brantford: 1) establish the degree to which the COMMIT met the needs of smokers for assistance in quitting; 2) identify the factors that inhibited or facilitated program success; and 3) consider the implications for community mobilization for smoking cessation. Findings in each of these areas are discussed. This work seeks to contribute to knowledge development in health promotion at the level of theory and method, as well as substantively in terms of the design and implementation of community health promotion interventions. A critical-interpretive methodology is advanced as being consistent with the 'new' health promotion, based on a review of the literature on social theory which also argues for an explicit critical and emancipatory orientation to theory and practice in health promotion. These approaches are applied to the examination of a community-level smoking cessation intervention. Chapter 9 contains a critical sociological examination of the nature of tobacco control, drawing upon the work of Goffman.Doctor of Philosophy (PhD

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as publishe

Celebrating Risk: The Politics of Self-Branding, Transgression & Resistance in Public Health

Persons \u27branded\u27 as dangerous to the public\u27s health often try to hide their status (as smokers, as HIV positive, etc). Yet, a small but growing subgroup has re-appropriated stigma symbols and voluntarily branded themselves as \u27marked\u27 individuals, rebellious, transgressive and refusing to be shamed by their status. In this article we examine voluntary branding as acts of resistance, paying particular attention to bodily practices that disrupt dominant aesthetic and moral/political sensibilities. We draw on our research and observations in the realms of smoking and bareback sex to illustrate and address broader issues of branding the self, aesthetics and the politics of resistance, surveillance, and transgression. Drawing on the work of Goffman, Bourdieu and Foucault, we examine the interpenetration of class, physical and social capital, and unequal social relations. While these works are often used to celebrate resistance, we argue, following Fiske, that it should not be romanticized as inherently liberating

Multiple timescales in a model for DNA denaturation dynamics

The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect this symmetry. Linking dissipation via untwist is allowed only at the two ends of the double strand. The result is a slow denaturation characterized by two time scales that depend on the chain length $L$. In a regime up to a first characteristic time $\tau_1\sim L^{2.15}$ the chain embodies an increasing number of small bubbles. Then, in a second regime, bubbles coalesce and form entropic barriers that effectively trap residual double-stranded segments within the chain, slowing down the relaxation to fully molten configurations, which takes place at $\tau_2\sim L^3$. This scenario is different from the picture in which the helical constraints are neglected.Comment: 9 pages, 5 figure

The Ecology of Health Service Utilization In Grenada, West Indies

It is widely accepted that the home environment may act as a socio-geographic focus of both disease transmission and of learned health behaviour. Households also appear to be units of convergence for factors identified in the literature as relating to the utilization of health services. This thesis is devoted to an examination of the role of the home environment, as well as of personal characteristics and accessibility, in the utilization of health services in Grenada, West Indies. The theoretical framework that informs this work is a holistic systems-orientated Socio-Ecological Model of Utilization. The empirical analysis draws upon the results of a detailed household survey conducted in five communities on the western portion of the island. Visits to homes containing children less than eight years of age isolated socio-demographic characteristics and information pertaining to residential mobility, household physical and behavioural environment, accessibility, self-reported morbidity and self-reported utilization. Records of patient visits over the previous two years for non-trauma events were abstracted from the medical records of area clinics, hospitals and physicians attending to the sample communities. Bivariate analyses between components of variables were conducted at both household and individual service use levels. These indicated that 1) service utilization was highly clustered around "high user" households and individuals; 2) considerable discrepancies emerged between self-reported and actual utilization; 3) the complexity of relationships between elements of the home environment was highlighted; and 4) there was a consistency with which certain elements of the home environment were statistically associated with health service use across a wide spectrum of illnesses. These observations were further confirmed in multivariate analyses, in which a small number of variables were able to retrospectively predict the presence or absence of service use by both adults and children with a high degree of model specificity and sensitivity. The implications of this work for development and health care planning in Grenada is discussed. The meaningful application of this work in Grenada is seen to hinge upon the extent to which relevant variables are amenable to change or act as proxy variables whose underlying nature of association with utilization remains to be adequately explored. A number of suggestions are advanced concerning the manner in which the study of health service utilization might be approached in the future.ThesisMaster of Arts (MA

Reaching for Environmental Health Justice: Canadian Experiences for a Comprehensive Research, Policy and Advocacy Agenda in Health Promotion

Spatial disparities in environmental quality and practices are contributing to rising health inequalities worldwide. To date, the field of health promotion has not contributed as significantly as it might to a systematic analysis of the physical environment as a determinant of health nor to a critique of inequitable environmental governance practices responsible for social injustice-particularly in the Canadian context. In this paper, we explore ways in which health promotion and environmental justice perspectives can be combined into an integrated movement for environmental health justice in health promotion. Drawing on Canadian experiences, we describe the historical contributions and limitations of each perspective in research, policy and particularly professional practice. We then demonstrate how recent environmental justice research in Canada is moving toward a deeper and multi-level analysis of environmental health inequalities, a development that we believe can inform a comprehensive research, policy and advocacy agenda in health promotion toward environmental health justice as a fundamental determinant of health. Lastly, we propose four key considerations for health promotion professionals to consider in advancing this movement

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure